BioC 3.0: CHECK report for categoryCompare on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch categoryCompare_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/categoryCompare.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘categoryCompare/DESCRIPTION’ ... OK
* this is package ‘categoryCompare’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘categoryCompare’ can be installed ... [33s/48s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.ccCompareGO: no visible binding for global variable ‘GOBPPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOMFPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOCCPARENTS’
.ccCompareGO: no visible binding for global variable ‘GOTERM’
.ccCompareKEGG: no visible binding for global variable
  ‘KEGGPATHID2NAME’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [44s/44s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/categoryCompare.Rcheck/00check.log’
for details.

* installing *source* package ‘categoryCompare’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘XMLRPC’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (categoryCompare)

name	user	system	elapsed
GENccEnrichResult-class	1.255	0.045	1.305
HyperGParamsCC-class	0.003	0.000	0.003
HyperGResultCC-class	0.002	0.000	0.003
breakEdges-methods	1.420	0.031	1.455
breakEdges	0	0	0
ccCompare	1.222	0.021	1.243
ccCompareCollection-class	0.001	0.000	0.001
ccCompareResult-class	0.002	0.001	0.001
ccData	1.282	0.030	1.313
ccEnrich	0.695	0.019	0.714
ccEnrichCollection-class	4.075	0.078	4.153
ccEnrichResult-class	4.862	0.047	4.908
ccGeneList-class	0.758	0.022	0.780
ccOptions-class	0.040	0.002	0.053
ccOutCyt-methods	0.001	0.000	0.001
ccSigList-class	0.001	0.000	0.001
cytOutData-methods	0.001	0.000	0.001
cytOutNodes-methods	0.001	0.000	0.002
hyperGTestCC	1.172	0.047	1.218
mergeLists-methods	1.570	0.033	1.604
mergedData-class	0.833	0.032	0.865
minCount	3.112	0.074	3.189
minNodes	0.001	0.000	0.001
pvalueType	4.341	0.040	4.382
show-methods	0.001	0.000	0.001

BioC 3.0: CHECK report for categoryCompare on perceval

Summary

Command output